However, the Wee Country boss hopes that Sunday's encounter with Costa Rica is not the 38-year-old's final game for his nation.
Hughes, Northern Ireland's most capped defender ever, is expected to make his 112th appearance for his country, just seven short of equalling Pat Jennings's overall record.
The Hearts man is yet to determine whether he will carry on his career after the current tour, though his club side appear willing to offer him fresh terms should he decide to continue.
"I would like Aaron to play as long as possible - he's so close to the record," O'Neill told Sky Sports News. "He can still play, hold his own, I've watched him in the Scottish Premiership this year. Aaron has earned the right to make that decision.
"I think the second half of the season has been good for him. The problem Aaron had was the frustration of the injuries. He was coming back, breaking down, he probably thought, 'I'm not proving to be much value to the club'. That's the type of guy Aaron is.
"I know they would be very keen for him to sign again at Hearts. I think it has to be right for him. I think he needs probably a wee bit of evaluation, 'Do I want to go on?' It's 20 years solid of first-team football, hotels, international football.
"Aaron, for me, is still capable of playing on, not only at club level but at international level. I genuinely really hope he does. If he made the decision to retire, I'd be disappointed because I want him in the squad but I also respect that what he's given us has been phenomenal."
Hughes made his debut for Northern Ireland in 1998, against Slovakia.